Add Dssp #50714
Add Dssp #50714
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Package(s) built are ready for inspection:
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| build: | ||
| - {{ compiler('c') }} | ||
| - {{ compiler('cxx') }} | ||
| - boost-cpp |
There was a problem hiding this comment.
Only 'make' and the compilers should be in 'build'. The libraries should be in 'host'
| about: | ||
| home: http://swift.cmbi.ru.nl/gv/dssp/ | ||
| summary: 'Secondary structure assignment' | ||
| license: Boost |
Co-authored-by: Martin Grigorov <[email protected]>
Co-authored-by: Martin Grigorov <[email protected]>
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There is a recipe in conda-forge for it already: https://anaconda.org/conda-forge/dssp |
📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces several significant changes to the Possibly related PRs
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Actionable comments posted: 7
🧹 Outside diff range and nitpick comments (11)
recipes/dssp/build.sh (2)
19-21: Quote the uname command to prevent word splittingThe
unamecommand should be quoted.Apply this fix:
-if [ `uname -s` = "Darwin" ]; then +if [ "`uname -s`" = "Darwin" ]; then🧰 Tools
🪛 Shellcheck
[warning] 19-19: Quote this to prevent word splitting.
(SC2046)
1-23: Package placement in bioconda is appropriateAlthough DSSP exists in conda-forge, its placement in bioconda is appropriate as it's directly related to biological sciences (protein structure analysis).
🧰 Tools
🪛 Shellcheck
[warning] 19-19: Quote this to prevent word splitting.
(SC2046)
recipes/tamper/meta.yaml (2)
15-16: Consider removing run_exports for this Python package.The
run_exportswithpin_subpackageis typically used for compiled libraries to ensure ABI compatibility. For a Python package marked asnoarch: generic, this level of version pinning might be unnecessarily restrictive and could complicate dependency resolution.build: number: 1 noarch: generic - run_exports: - - {{ pin_subpackage(name, max_pin='x.x') }}
33-36: Enhance test coverage.Current tests only verify command existence. Consider adding:
- Import tests for Python modules
- Basic functionality tests with minimal example data
test: + imports: + - tamper commands: - train_tAMPer -h - predict_tAMPer -h + - python -c "from tamper import predict; assert predict"recipes/tamper/build.sh (2)
3-6: Add error checking and verbose output for directory creation.While the directory structure is correct, the script could be more robust with error checking and verbose output.
-mkdir -p ${PREFIX}/bin/ -mkdir -p ${PREFIX}/share/tamper/ -mkdir -p ${PREFIX}/share/tamper/src/ -mkdir -p ${PREFIX}/share/tamper/checkpoints/trained +mkdir -pv ${PREFIX}/bin/ || exit 1 +mkdir -pv ${PREFIX}/share/tamper/ || exit 1 +mkdir -pv ${PREFIX}/share/tamper/src/ || exit 1 +mkdir -pv ${PREFIX}/share/tamper/checkpoints/trained || exit 1
11-15: Fix typo and optimize permission commands.The comment contains a typo, and the chmod commands can be combined for efficiency.
-#This allows src code to be executbale for user and group -chmod -R u+x ${PREFIX}/share/tamper/src/ -chmod -R g+x ${PREFIX}/share/tamper/src/ +# This allows source code to be executable for user and group +chmod -R ug+x ${PREFIX}/share/tamper/src/ || exit 1recipes/dssp/meta.yaml (4)
3-3: Improve attribution comment clarity.The current comment should be more specific about what modifications were made to the original recipe. This helps future maintainers understand the differences.
-# This file, the patch file and build file were taken from conda salilab channel's recipes - please see https://github.com/salilab/conda-recipes for more. +# This recipe is based on the salilab channel's DSSP recipe (https://github.com/salilab/conda-recipes) with the following modifications: +# - Updated for version 3.0.0 +# - Modified dependencies structure +# For more details, see the original recipe.
12-12: Complete the patch file documentation.The comment for the patch file is incomplete and should provide more context about its purpose.
- - dssp-boost-tr1.patch #Rebuild with latest gcc and boost - this was taken from the + - dssp-boost-tr1.patch # Patch to update std::tr1 namespace usage to std namespace for compatibility with modern gcc and boost
50-52: Enhance test coverage.The current test only checks if the command runs. Consider adding more comprehensive tests:
- Test actual functionality with a small PDB file
- Verify output format
- Test help command
test: + files: + - test.pdb commands: - mkdssp --version + - mkdssp --help + - mkdssp -i test.pdb -o test.dsspWould you like me to help create a minimal test.pdb file and expected output for testing?
1-52: Consider using conda-forge package instead of creating a new recipe.As mentioned by @martin-g, there's already a DSSP package in conda-forge (https://anaconda.org/conda-forge/dssp). According to Bioconda guidelines, new recipes not directly related to biological sciences should be submitted to conda-forge instead.
Consider either:
- Using the existing conda-forge package as a dependency
- Contributing improvements to the conda-forge recipe
- Providing strong justification for maintaining a separate package in Bioconda
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/dssp/dssp-boost-tr1.patch (1)
65-65: Fix typo in variable name.There's a typo in the variable name:
alhpashould bealpha.- double alhpa = 360; + double alpha = 360;
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (5)
recipes/dssp/build.sh(1 hunks)recipes/dssp/dssp-boost-tr1.patch(1 hunks)recipes/dssp/meta.yaml(1 hunks)recipes/tamper/build.sh(1 hunks)recipes/tamper/meta.yaml(1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/dssp/build.sh
[warning] 19-19: Quote this to prevent word splitting.
(SC2046)
🪛 yamllint
recipes/dssp/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/tamper/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (10)
recipes/dssp/build.sh (5)
1-4: LGTM: Proper script initialization
Good use of set -e to ensure the script fails immediately if any command fails.
5-6: LGTM: Proper dynamic linking setup
Correctly removes static linking which is appropriate for conda packages.
23-23: LGTM: Proper parallel build setup
16-21: Verify the clang warning suppression flag
The -Wno-enum-constexpr-conversion flag is specific to clang. Let's ensure it's supported by the version of clang being used.
#!/bin/bash
# Description: Check if the warning flag is supported by clang
# Test: Try compiling a minimal program with the flag
echo "#include <iostream>" > test.cpp
${CXX} -Wno-enum-constexpr-conversion -c test.cpp 2>&1 || echo "Warning flag not supported"
rm -f test.cpp test.o🧰 Tools
🪛 Shellcheck
[warning] 19-19: Quote this to prevent word splitting.
(SC2046)
8-14: LGTM: Proper make configuration setup
Configuration correctly uses conda environment variables for paths and compiler settings.
Let's verify the Boost paths are correct:
recipes/tamper/build.sh (1)
1-34: Verify PR scope and dependencies.
This build script is for the tamper package, but the PR objectives mention adding DSSP. Please clarify:
- Is this file part of the intended scope of the PR?
- If yes, how does this relate to the DSSP addition mentioned in the PR objectives?
- Should there be any DSSP-related dependencies or integration points in this script?
recipes/dssp/dssp-boost-tr1.patch (4)
8-9: LGTM: Correctly modernizes tuple unpacking.
The change from std::tr1::tie to std::tie is appropriate as it moves away from the deprecated TR1 namespace to modern C++ standards.
20-21: LGTM: Consistent modernization of tuple usage.
The changes correctly update both the function signature and tuple creation:
- Return type changed from
std::tr1::tupletostd::tuple - Tuple creation updated from
std::tr1::make_tupletostd::make_tuple
Also applies to: 29-30
62-63: LGTM: Consistent method modernization.
The changes correctly update both the method declaration and implementation to use standard C++ tuples instead of TR1.
Also applies to: 71-72, 83-84
41-42: LGTM: Proper header modernization and consistent declarations.
The changes correctly:
- Replace the deprecated Boost TR1 tuple header with the standard C++ tuple header
- Update the function declaration to match its implementation
Let's verify no other TR1 dependencies remain:
Also applies to: 50-51
✅ Verification successful
The previous search might have been too narrow. Let's try with a broader pattern and also use ast-grep to specifically look for boost/tr1 includes. This will help us verify if the TR1 modernization is complete across the codebase.
The search results show that TR1 dependencies are only present in the patch file recipes/dssp/dssp-boost-tr1.patch which is actually the patch that's making the changes to remove those TR1 dependencies. The patch is replacing:
#include <boost/tr1/tuple.hpp>with#include <tuple>- Several uses of
std::tr1::namespace with standard C++ equivalents
This indicates that the review comment is correct - the changes are properly modernizing the code by replacing Boost TR1 with standard C++ headers and namespaces.
LGTM: TR1 modernization changes are complete and consistent
The patch correctly removes all Boost TR1 dependencies in favor of standard C++ equivalents. No remaining TR1 dependencies were found in the codebase.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for any remaining TR1 dependencies
rg --type cpp "tr1"
Length of output: 19
Script:
#!/bin/bash
# Search for any remaining TR1 dependencies with case-insensitive and broader pattern
rg -i "boost.*tr1|tr1"
# Also check specifically for any remaining boost/tr1 includes
ast-grep --pattern '#include <boost/tr1/$_>'
Length of output: 120729
| - python >=3.9 | ||
| run: | ||
| - biopython | ||
| - dssp |
There was a problem hiding this comment.
Use conda-forge dssp package instead of adding a new one.
According to the PR comments, DSSP is already available in conda-forge (https://anaconda.org/conda-forge/dssp). Instead of creating a new package in bioconda, consider using the existing conda-forge package by adding the channel specification:
- dssp
+ conda-forge::dssp📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - dssp | |
| - conda-forge::dssp |
| - pytorch | ||
| - pytorch_cluster | ||
| - pytorch_geometric | ||
| - torch-scatter |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add version constraints for PyTorch dependencies.
The PyTorch ecosystem packages often have strict version compatibility requirements. Missing version constraints could lead to dependency conflicts.
- pytorch
- pytorch_cluster
- pytorch_geometric
- torch-scatter
+ pytorch>=2.0
+ pytorch_cluster>=1.6
+ pytorch_geometric>=2.3
+ torch-scatter>=2.1📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - pytorch | |
| - pytorch_cluster | |
| - pytorch_geometric | |
| - torch-scatter | |
| - pytorch>=2.0 | |
| - pytorch_cluster>=1.6 | |
| - pytorch_geometric>=2.3 | |
| - torch-scatter>=2.1 |
| #Adding python executable for the script to work | ||
| echo "#!/bin/bash" > ${PREFIX}/bin/predict_tAMPer | ||
| echo "python ${PREFIX}/share/tamper/src/predict_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/predict_tAMPer | ||
|
|
||
| echo "#!/bin/bash" > ${PREFIX}/bin/train_tAMPer.py | ||
| echo "python ${PREFIX}/share/tamper/src/train_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/train_tAMPer | ||
|
|
There was a problem hiding this comment.
Improve script creation and fix inconsistent naming.
Several issues need attention:
train_tAMPer.pyhas a .py extension despite being a bash script- Using echo for script creation is error-prone
- Missing error checking
-echo "#!/bin/bash" > ${PREFIX}/bin/predict_tAMPer
-echo "python ${PREFIX}/share/tamper/src/predict_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/predict_tAMPer
-
-echo "#!/bin/bash" > ${PREFIX}/bin/train_tAMPer.py
-echo "python ${PREFIX}/share/tamper/src/train_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/train_tAMPer
+# Create predict_tAMPer wrapper
+cat > "${PREFIX}/bin/predict_tAMPer" << 'EOF' || exit 1
+#!/bin/bash
+python "${PREFIX}/share/tamper/src/predict_tAMPer.py" "$@"
+EOF
+
+# Create train_tAMPer wrapper (removed .py extension)
+cat > "${PREFIX}/bin/train_tAMPer" << 'EOF' || exit 1
+#!/bin/bash
+python "${PREFIX}/share/tamper/src/train_tAMPer.py" "$@"
+EOF📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| #Adding python executable for the script to work | |
| echo "#!/bin/bash" > ${PREFIX}/bin/predict_tAMPer | |
| echo "python ${PREFIX}/share/tamper/src/predict_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/predict_tAMPer | |
| echo "#!/bin/bash" > ${PREFIX}/bin/train_tAMPer.py | |
| echo "python ${PREFIX}/share/tamper/src/train_tAMPer.py \"\$@\"" >> ${PREFIX}/bin/train_tAMPer | |
| #Adding python executable for the script to work | |
| # Create predict_tAMPer wrapper | |
| cat > "${PREFIX}/bin/predict_tAMPer" << 'EOF' || exit 1 | |
| #!/bin/bash | |
| python "${PREFIX}/share/tamper/src/predict_tAMPer.py" "$@" | |
| EOF | |
| # Create train_tAMPer wrapper (removed .py extension) | |
| cat > "${PREFIX}/bin/train_tAMPer" << 'EOF' || exit 1 | |
| #!/bin/bash | |
| python "${PREFIX}/share/tamper/src/train_tAMPer.py" "$@" | |
| EOF |
| chmod +x ${PREFIX}/bin/predict_tAMPer | ||
| chmod +x ${PREFIX}/bin/train_tAMPer | ||
|
|
||
| #Verify permissions | ||
| echo "Permissions after chmod:" | ||
| ls -l ${PREFIX}/share/tamper/src/ |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve permission setting and verification.
The current verification process could be more robust with proper error checking and validation.
-chmod +x ${PREFIX}/bin/predict_tAMPer
-chmod +x ${PREFIX}/bin/train_tAMPer
+chmod +x "${PREFIX}/bin/predict_tAMPer" || exit 1
+chmod +x "${PREFIX}/bin/train_tAMPer" || exit 1
-#Verify permissions
-echo "Permissions after chmod:"
-ls -l ${PREFIX}/share/tamper/src/
+# Verify executables are properly set up
+for cmd in predict_tAMPer train_tAMPer; do
+ if [ ! -x "${PREFIX}/bin/${cmd}" ]; then
+ echo "Error: ${cmd} is not executable" >&2
+ exit 1
+ fi
+done📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| chmod +x ${PREFIX}/bin/predict_tAMPer | |
| chmod +x ${PREFIX}/bin/train_tAMPer | |
| #Verify permissions | |
| echo "Permissions after chmod:" | |
| ls -l ${PREFIX}/share/tamper/src/ | |
| chmod +x "${PREFIX}/bin/predict_tAMPer" || exit 1 | |
| chmod +x "${PREFIX}/bin/train_tAMPer" || exit 1 | |
| # Verify executables are properly set up | |
| for cmd in predict_tAMPer train_tAMPer; do | |
| if [ ! -x "${PREFIX}/bin/${cmd}" ]; then | |
| echo "Error: ${cmd} is not executable" >&2 | |
| exit 1 | |
| fi | |
| done |
| cp -r src/. ${PREFIX}/share/tamper/src/ | ||
| cp -r checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained | ||
| ls ${PREFIX}/share/tamper/src/ |
There was a problem hiding this comment.
Add source directory verification and error checking for file copying.
The current implementation doesn't verify source directories exist or handle copy errors properly.
+# Verify source directories exist
+[ ! -d "src" ] && echo "Error: src directory not found" && exit 1
+[ ! -d "checkpoints/trained" ] && echo "Error: checkpoints/trained directory not found" && exit 1
+
-cp -r src/. ${PREFIX}/share/tamper/src/
-cp -r checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained
-ls ${PREFIX}/share/tamper/src/
+cp -rv src/. ${PREFIX}/share/tamper/src/ || exit 1
+cp -rv checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained || exit 1
+
+# Verify files were copied
+echo "Verifying copied files..."
+[ -z "$(ls -A ${PREFIX}/share/tamper/src/)" ] && echo "Error: No files copied to src directory" && exit 1
+[ -z "$(ls -A ${PREFIX}/share/tamper/checkpoints/trained/)" ] && echo "Error: No files copied to checkpoints directory" && exit 1📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| cp -r src/. ${PREFIX}/share/tamper/src/ | |
| cp -r checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained | |
| ls ${PREFIX}/share/tamper/src/ | |
| # Verify source directories exist | |
| [ ! -d "src" ] && echo "Error: src directory not found" && exit 1 | |
| [ ! -d "checkpoints/trained" ] && echo "Error: checkpoints/trained directory not found" && exit 1 | |
| cp -rv src/. ${PREFIX}/share/tamper/src/ || exit 1 | |
| cp -rv checkpoints/trained/. ${PREFIX}/share/tamper/checkpoints/trained || exit 1 | |
| # Verify files were copied | |
| echo "Verifying copied files..." | |
| [ -z "$(ls -A ${PREFIX}/share/tamper/src/)" ] && echo "Error: No files copied to src directory" && exit 1 | |
| [ -z "$(ls -A ${PREFIX}/share/tamper/checkpoints/trained/)" ] && echo "Error: No files copied to checkpoints directory" && exit 1 |
| about: | ||
| home: http://swift.cmbi.ru.nl/gv/dssp/ | ||
| summary: 'Secondary structure assignment' | ||
| license: Boost | ||
| description: > | ||
| The DSSP program was designed by Wolfgang Kabsch and Chris Sander to | ||
| standardize secondary structure assignment. DSSP is a database of secondary | ||
| structure assignments (and much more) for all protein entries in the Protein | ||
| Data Bank (PDB). DSSP is also the program that calculates DSSP entries from | ||
| PDB entries. DSSP does not predict secondary structure. | ||
|
|
||
| Note that this is a very old version of DSSP, which we have used in the | ||
| past. It is kept here in the hope that others may find it useful - but | ||
| it may not work on newer systems (e.g. Apple Silicon Macs). We recommend | ||
| using the most recent version of DSSP instead. | ||
| See [the DSSP website](http://swift.cmbi.ru.nl/gv/dssp/) for more details. | ||
|
|
||
| If you have problems with this conda package, please | ||
| [open an issue](https://github.com/salilab/conda-recipes/issues). | ||
|
|
There was a problem hiding this comment.
🛠️ Refactor suggestion
Update package metadata for better compliance.
Several improvements are needed in the about section:
- Add
license_filefield - Use HTTPS for the home URL
- Consider adding
doc_urlanddev_urlfields - The warning about old version seems inconsistent with version 3.0.0
about:
- home: http://swift.cmbi.ru.nl/gv/dssp/
+ home: https://swift.cmbi.ru.nl/gv/dssp/
summary: 'Secondary structure assignment'
license: Boost
+ license_file: LICENSE
+ doc_url: https://swift.cmbi.ru.nl/gv/dssp/DSSP_3.html
+ dev_url: https://github.com/cmbi/dssp
description: >
The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
standardize secondary structure assignment. DSSP is a database of secondary
structure assignments (and much more) for all protein entries in the Protein
Data Bank (PDB). DSSP is also the program that calculates DSSP entries from
PDB entries. DSSP does not predict secondary structure.
- Note that this is a very old version of DSSP, which we have used in the
- past. It is kept here in the hope that others may find it useful - but
- it may not work on newer systems (e.g. Apple Silicon Macs). We recommend
- using the most recent version of DSSP instead.
+ This is version 3.0.0 of DSSP, which includes modern C++ standards support
+ and compatibility with newer systems.
See [the DSSP website](http://swift.cmbi.ru.nl/gv/dssp/) for more details.
- If you have problems with this conda package, please
- [open an issue](https://github.com/salilab/conda-recipes/issues).
+ If you have problems with this conda package, please open an issue at
+ https://github.com/bioconda/bioconda-recipes/issuesCommittable suggestion skipped: line range outside the PR's diff.
| requirements: | ||
| build: | ||
| - {{ compiler('c') }} | ||
| - {{ compiler('cxx') }} | ||
| - boost-cpp | ||
| - zlib | ||
| - bzip2 | ||
| - make | ||
| run: | ||
| - {{ pin_compatible('boost-cpp') }} |
There was a problem hiding this comment.
Restructure dependencies sections.
Libraries should be in the host section, not in build. Only build tools like make and compilers should be in the build section. This ensures proper build environment setup.
requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- - boost-cpp
- - zlib
- - bzip2
- make
+ host:
+ - boost-cpp
+ - zlib
+ - bzip2
run:
- {{ pin_compatible('boost-cpp') }}
+ - zlib
+ - bzip2📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| requirements: | |
| build: | |
| - {{ compiler('c') }} | |
| - {{ compiler('cxx') }} | |
| - boost-cpp | |
| - zlib | |
| - bzip2 | |
| - make | |
| run: | |
| - {{ pin_compatible('boost-cpp') }} | |
| requirements: | |
| build: | |
| - {{ compiler('c') }} | |
| - {{ compiler('cxx') }} | |
| - make | |
| host: | |
| - boost-cpp | |
| - zlib | |
| - bzip2 | |
| run: | |
| - {{ pin_compatible('boost-cpp') }} | |
| - zlib | |
| - bzip2 |
I added DSSP (https://swift.cmbi.umcn.nl/gv/dssp/index.html) with slightly changing the script from https://anaconda.org/salilab/dssp.
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...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
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